Contacts of the strand formed by residues 395 - 399 (chain A) in PDB entry 2R8J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A VAL* 4.1 10.8 - - + -
394A SER* 1.3 83.3 - - - +
396A MET* 1.3 60.1 + - - +
423A LEU* 3.5 13.1 - - + +
426A ARG* 3.7 44.0 - - - +
427A ILE* 3.5 30.5 - - + +
430A LEU* 3.5 31.9 - - + -
502A THR* 3.4 5.0 - - - -
503A ILE* 3.1 46.6 + - + +
506A PHE* 3.8 9.9 - - + -
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Residues in contact with MET 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER* 5.5 0.2 + - - -
395A MET* 1.3 75.6 - - - +
397A SER* 1.3 73.7 + - - +
398A ASN* 2.9 37.7 - - - +
422A GLU* 4.9 2.1 - - - +
423A LEU* 4.1 2.5 - - - +
426A ARG* 3.9 17.0 + - - +
498A LYS* 4.8 6.3 - - - +
500A SER* 4.1 16.6 - - - -
501A MET 3.4 6.3 - - - +
502A THR* 3.5 22.4 - - + +
7U T 5.0 8.3 - - + +
8U C 4.1 15.5 + - - +
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Residues in contact with SER 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 3.5 7.1 - - - +
396A MET* 1.3 80.5 - - - +
398A ASN* 1.3 60.2 + - - +
419A PHE* 3.3 42.0 + - - -
422A GLU* 3.4 23.9 + - - -
423A LEU* 3.9 19.1 - - - -
501A MET 3.1 24.2 + - - -
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LYS* 3.4 24.2 + - - +
396A MET* 2.9 29.4 - - + +
397A SER* 1.3 72.3 - - - +
399A LYS* 1.3 71.0 + - - +
400A ASN* 2.9 28.6 + - - +
419A PHE* 3.5 7.6 - - - -
498A LYS* 3.5 11.7 + - - +
499A LEU 3.5 6.3 - - - +
500A SER* 3.1 27.4 - - - -
7U T 3.3 28.0 + - - -
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A TRP* 4.0 5.7 - - - -
121A VAL* 3.0 33.8 + - - +
122A GLU 4.4 3.8 - - - -
124A HIS 2.7 28.5 + - - +
125A LYS* 4.7 7.3 - - + +
398A ASN* 1.3 84.1 - - - +
400A ASN* 1.3 71.7 + - - +
401A LEU* 2.8 40.0 + - + +
402A ARG 5.7 1.1 - - - +
415A TRP* 3.9 24.7 - - + -
419A PHE* 3.9 17.5 - - + -
499A LEU* 3.3 15.6 + - + +
6U C 5.0 6.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il